Biology subjects

Yuan, J.

Publications and source records attributed to Yuan, J..

At least 73 records · Page 4Linked to original sources

bioRxiv2024

Enhanced bacterial chemotaxis in confined microchannels: Optimal performance in lane widths matching circular swimming radius

Understanding bacterial behavior in confined environments is helpful for elucidating microbial ecology and developing strategies to manage bacterial infections. While extensive research has focused on bacterial motility on surfaces and in porous media, chemotaxis in confined spaces remains poorly understood. Here, we investigate the chemotaxis of Escherichia coli within microfluidic lanes under a linear concentration gradient of L-aspartate. We demonstrate that E. coli exhibits significantly enhanced chemotaxis in lanes with sidewalls compared to open surfaces. We attribute this phenomenon primarily to the intrinsic chiral clockwise circular motion of surface-swimming bacteria and the subsequent alignment effect upon collision with the sidewalls. By varying lane widths, we identify that an 8 m width--approximating the radius of bacterial circular swimming on surfaces--maximizes chemotactic drift velocity. These results are supported by both experimental observations and stochastic simulations, establishing a clear proportional relationship between optimal lane width and the radius of bacterial circular swimming. Further geometric analysis provides an intuitive understanding of this phenomenon. Our results may offer insights into bacterial navigation in complex biological environments such as host tissues and biofilms, providing a preliminary step toward exploring microbial ecology in confined habitats and potential strategies for controlling bacterial infections.

biophysics↗

bioRxiv2024

Maternal immunity protects offspring from enteric viral infection without negatively affecting humoral immune memory

Mother-to-offspring transfer of antibodies protects newborns during the critical phase of early life, preventing both infection and inflammation. Whether and how pre-existing passive immunity actively shapes immune memory formation in neonates remains unclear. Using a murine neonatal Rotavirus infection model in combination with cross-foster approaches and genetic models, we disentangled the contribution of maternal IgA and IgG to neonatal immune outcomes. While breastmilk antigen specific IgA is responsible for protection from Rotavirus infection, antigen specific IgG delays pup-intrinsic humoral immune induction to after weaning. Importantly, pre-existing maternal immunity delays and constrains, rather than ablates, long term humoral immunity. Together, our data move beyond a binary view of passive immunity as protective versus inhibitory, providing a more nuanced understanding in which breastmilk antibodies actively program the neonatal response for optimal immediate protection and long-term immune education in the growing organism.

immunology↗

bioRxiv2024

SOX21 suppresses GBM growth by repressing AP-1 regulated target genes

BackgroundTreatment-resistant glioblastoma stem cells (GSCs) drive glioblastoma (GBM) growth and recurrence. Thus, targeting the molecular machinery that sustains GSCs in an undifferentiated and self-renewing state is a promising therapeutic strategy. The transcription factor SOX21 effectively suppresses the tumorigenic capacity of GSCs. However, the mechanism by which SOX21 impedes GSC features is unknown. MethodsPatient-derived GSCs were engineered with a transgenic TetOn system to enable inducible expression of SOX21 or appropriate controls. The capacity of SOX21 to incapacitate GSCs was assessed using in vitro cell culture models and orthotopic mouse models. Cellular and genome-wide techniques, including RNA-seq, ChIP-seq, and ATAC-seq, were employed to examine the mechanisms by which SOX21 regulates GSCs. ResultsWe show that SOX21 expression in primary GSCs induces an anti-tumorigenic transcriptional program, aligning with clinical data showing a positive correlation between SOX21 levels and improved GBM patient survival. Induced SOX21 expression in GSCs within pre-established GBM reduces their capacity to sustain tumor growth and significantly extends the survival of the transplanted mice. Mechanistically, SOX21 functions as a tumor suppressor by binding a large set of AP-1-targeted chromatin regions, leading to epigenetic repression of AP-1-activated genes that support GSC survival and proliferation. Consistently, the anti-tumorigenic activities of SOX21 are replicated by AP-1 inhibitors, while overexpression of the AP-1 family member, c-JUN, counteracts these effects. ConclusionOur findings identify SOX21 as a key regulator that prevents GSC malignancy by targeting and repressing an AP-1-driven, tumor-promoting gene expression program. These results highlight SOX21-regulated pathways as promising therapeutic targets for GBM. Key PointsO_LIInduced SOX21 expression suppresses GSCs and inhibits the growth of established GBM C_LIO_LISOX21 acts as a tumor suppressor in GSCs by directly repressing AP-1-driven genes C_LIO_LIPharmacological inhibition of AP-1 mimics SOX21 activity in GSCs C_LI Importance of the StudyGBM is the most common and aggressive malignant brain tumor in adults. Recurrence following treatment often stems from the failure of therapeutic interventions to effectively target GSCs, which serve as the primary reservoir for tumor regrowth. The resilience of GSCs to treatment is partly due to the inactivation of intrinsic tumor suppressor programs that would otherwise direct GSCs to cellular senescence and death. This study demonstrates that increased expression levels of the tumor suppressor SOX21 in pre-established GBM disrupt tumor progression by disabling self-renewing GSCs. We show that SOX21 exerts its tumor-suppressive function by targeting and repressing an AP-1-driven gene network, which is a key regulator of GSC maintenance and proliferation. By uncovering the molecular mechanisms through which SOX21 controls GSC biology, our findings provide valuable insights for basic cancer research and may inform the development of novel therapeutic strategies for GBM.

cancer biology↗

bioRxiv2024

Transcriptional pathobiology and multi-omics predictors for Parkinson's disease

Early diagnosis and biomarker discovery to bolster the therapeutic pipeline for Parkinsons disease (PD) are urgently needed. In this study, we leverage the large-scale whole-blood total RNA-seq dataset from the Accelerating Medicine Partnership in Parkinsons Disease (AMP PD) program to identify PD-associated RNAs, including both known genes and novel circular RNAs (circRNA) and enhancer RNAs (eRNAs). There were 1,111 significant marker RNAs, including 491 genes, 599 eRNAs, and 21 circRNAs, that were first discovered in the PPMI cohort (FDR < 0.05) and confirmed in the PDBP/BioFIND cohorts (nominal p < 0.05). Functional enrichment analysis showed that the PD-associated genes are involved in neutrophil activation and degranulation, as well as the TNF-alpha signaling pathway. We further compare the PD-associated genes in blood with those in post-mortem brain dopamine neurons in our BRAINcode cohort. 44 genes show significant changes with the same direction in both PD brain neurons and PD blood, including neuroinflammation-associated genes IKBIP, CXCR2, and NFKBIB. Finally, we built a novel multi-omics machine learning model to predict PD diagnosis with high performance (AUC = 0.89), which was superior to previous studies and might aid the decision-making for PD diagnosis in clinical practice. In summary, this study delineates a wide spectrum of the known and novel RNAs linked to PD and are detectable in circulating blood cells in a harmonized, large-scale dataset. It provides a generally useful computational framework for further biomarker development and early disease prediction. Significance statementEarly and accurate diagnosis of Parkinsons disease (PD) is urgently needed. However, biomarkers for early detection of PD are still lacking. Also, the limit of sample size remains one of the main pitfalls of current PD biomarker studies. We employed an analysis of large-scale whole-blood RNA-seq data. By identifying 1,111 significant marker RNAs, we establish a robust foundation for early PD detection, which implicated in neutrophil activation, degranulation, and TNF-alpha signaling, offer unprecedented insights into PD pathogenesis. Our multi-omics machine learning model, boasting an AUC of 0.89, outperforms previous studies, promising a transformative tool for precise PD diagnosis in clinical settings. This study marks a pivotal step toward enhanced biomarker development and early disease prediction.

neuroscience↗

bioRxiv2024

PhyloFunc: Phylogeny-informed Functional Distance as a New Ecological Metric for Metaproteomic Data Analysis

BackgroundBeta-diversity is a fundamental ecological metric for exploring dissimilarities between microbial communities. On the functional dimension, metaproteomics data can be used to quantify beta-diversity to understand how microbial community functional profiles vary under different environmental conditions. Conventional approaches to metaproteomic functional beta-diversity often treat protein functions as independent features, ignoring the evolutionary relationships among microbial taxa from which different proteins originate. A more informative functional distance metric that incorporates evolutionary relatedness is needed to better understand microbiome functional dissimilarities. ResultsHere, we introduce PhyloFunc, a novel functional beta-diversity metric that incorporates microbiome phylogeny to inform on metaproteomic functional distance. Leveraging the phylogenetic framework of weighted UniFrac distance, PhyloFunc innovatively utilizes branch lengths to weigh between-sample functional distances for each taxon, rather than differences in taxonomic abundance as in weighted UniFrac. Proof-of-concept using a simulated toy dataset and a real dataset from mouse inoculated with a synthetic gut microbiome and fed different diets show that PhyloFunc successfully captured functional compensatory effects between phylogenetically related taxa. We further tested a third dataset of complex human gut microbiomes treated with five different drugs to compare PhyloFuncs performance with other traditional distance methods. PCoA and machine learning-based classification algorithms revealed higher sensitivity of PhyloFunc in microbiome responses to paracetamol. We provide PhyloFunc as an open-source Python package (available at https://pydigger.com/pypi/PhyloFunc), enabling efficient calculation of functional beta-diversity distances between a pair of samples or the generation of a distance matrix for all samples within a dataset. ConclusionsUnlike traditional approaches that consider metaproteomics features as independent and unrelated, PhyloFunc acknowledges the role of phylogenetic context in shaping the functional landscape in metaproteomes. In particular, we report that PhyloFunc accounts for the functional compensatory effect of taxonomically related species. Its effectiveness, ecological relevance, and enhanced sensitivity in distinguishing group variations are demonstrated through the specific applications presented in this study.

bioinformatics↗

bioRxiv2024

Harnessing Data-Intelligence-Intensive Multi-Agent System for Life Science Research

Advancements in high-throughput sequencing technologies and artificial intelligence offer unprecedented opportunities for groundbreaking discoveries in bioinformatics research. However, the challenges of exponential growth of omics data and the rapid development of artificial intelligence technologies require automated big biological data analysis capability and interdisciplinary knowledge-driven scientific insight. Here we propose a data-intelligence-intensive bioinformatics copilot (Bio-Copilot) system that synergizes AI capabilities with human expertise to facilitate hypothesis-free exploratory research and inspire novel scientific insights in large-scale omics studies. Bio-Copilot forms high-quality intensive intelligence through close collaboration between multiple agents, driven by large language models (LLMs), and human experts. To augment the capabilities of Bio-Copilot, this study devises an agent group management strategy, an effective human-agent interaction mechanism, a shared interdisciplinary knowledge database, and continuous learning strategies for the agents. We comprehensively compare Bio-Copilot against GPT-4o and several leading AI agents across diverse bioinformatics tasks, using a broad range of evaluation metrics. Bio-Copilot achieves the overall state-of-the-art performance across all tasks, while showcases exceptional task completeness. Furthermore, in the application of constructing a large-scale human lung cell atlas, Bio-Copilot not only reproduces the intricate data integration process detailed in a seminal study but also introduces a hierarchical annotation strategy to capture the continuous nature of cellular states and uncovers the characteristics of rare cell types, highlighting its potential to unravel hidden complexities in biological systems. Beyond the technical achievements, this study also underscores the profound implications of integrating AI capabilities with expert knowledge in accelerating impactful biological discoveries and exploring uncharted territories in life sciences.

bioinformatics↗

bioRxiv2024

Repression of PRMT activities sensitize homologous recombination-proficient ovarian and breast cancer cells to PARP inhibitor treatment

Therapeutic epigenetic modulation is currently being evaluated in the clinic to sensitize homologous recombination (HR)-proficient tumors to PARP inhibitors. To broaden its clinical applicability and identify more effective combination strategies, we conducted a drug screen combining PARP inhibitors with 74 well-characterized epigenetic modulators targeting five major classes of epigenetic enzymes. Notably, both type I PRMT inhibitors and PRMT5 inhibitors scored highly in combination efficacy and clinical prioritization. PRMT inhibition significantly enhanced PARP inhibitor-induced DNA damage in HR-proficient ovarian and breast cancer cells. Mechanistically, PRMT suppression downregulates DNA damage repair genes and BRCAness-associated pathways, while also modulating intrinsic innate immune responses within cancer cells. Integrative analysis of large-scale genomic and functional datasets from TCGA and DepMap further supports PRMT1, PRMT4, and PRMT5 as promising therapeutic targets in oncology. Importantly, dual inhibition of PRMT1 and PRMT5 synergistically sensitizes tumors to PARP inhibitors. Collectively, our findings provide strong rationale for the clinical development of PRMT and PARP inhibitor combinations in HR-proficient ovarian and breast cancers.

cancer biology↗

bioRxiv2024

From gene to structure: Unraveling genomic dark matter in Ca. Accumulibacter

Candidatus Accumulibacter is a unique and pivotal genus of polyphosphate-accumulating organisms (PAOs) prevalent in wastewater treatment plants, and plays mainstay roles in the global phosphorus cycle. Whereas, the efforts toward a complete understanding of their genetic and metabolic characteristics are largely hindered by major limitations in existing sequence-based annotation methods, leaving more than half of their protein-encoding genes unannotated. To address the challenge, we developed a comprehensive approach integrating pangenome analysis, gene-based protein structure and function prediction, and metatranscriptomic analysis, extending beyond the constraints of sequence-centric methodologies. The application to Ca. Accumulibacter allowed the establishment of the pan-Ca. Accumulibacter proteome structure database, providing references for >200,000 proteins. Benchmarking on 28 Ca. Accumulibacter genomes showed major increases in the average annotation coverage from 51% to 83%. Genetic and metabolic characteristics that had eluded exploration via conventional methods were unraveled. For instance, the identification of a previously unknown phosphofructokinase gene suggests that all Ca. Accumulibacter encoded a complete Embden-Meyerhof-Parnas pathway. A previously defined homolog of phosphate-specific transport system accessory protein (PhoU) was actually an inorganic phosphate transport (Pit) accessory protein, regulating Pit instead of the high-affinity phosphate transport (Pst), a key to the emergence of the polyphosphate-accumulating trait of Ca. Accumulibacter. Additional lineage members were found encoding complete denitrification pathways. This study offers a readily usable and transferable tool for the establishment of high-coverage annotation reference databases for diverse cultured and uncultured bacteria, facilitating the exploration and understanding of genomic dark matter in the bacterial domain. SynopsisA integrated and advanced approach unraveling key genomic dark matter in Ca. Accumulibacter and readily applicable to diverse bacteria for customerized high-coverage annotation reference database establishment

genomics↗

bioRxiv2024

Atomic insights into the signaling landscape of E. coli PhoQ Histidine Kinase from Molecular Dynamics simulations

Bacteria rely on two-component systems to sense environmental cues and regulate gene expression for adaptation. The PhoQ/PhoP system exemplifies this crucial role, playing a key part in sensing magnesium (Mg2+) levels, antimicrobial peptides, mild acidic pH, osmotic upshift, and long-chain unsaturated fatty acids, promoting virulence in certain bacterial species. However, the precise details of PhoQ activation remain elusive. To elucidate PhoQs signaling mechanism at atomic resolution, we combined AlphaFold2 predictions with molecular modeling and carried out extensive Molecular Dynamics (MD) simulations. Our MD simulations revealed three distinct PhoQ conformations that were validated by experimental data. Notably, one conformation was characterized by Mg2+ bridging the acidic patch in the sensor domain to the membrane, potentially representing a repressed state. Furthermore, the high hydration observed in a putative intermediate state lends support to the hypothesis of water-mediated conformational changes during PhoQ signaling. Our findings not only revealed specific conformations within the PhoQ signaling pathway, but also hold significant promise for understanding the broader histidine kinase family due to their shared structural features. Our approach paves the way for a more comprehensive understanding of histidine kinase signaling mechanisms across various bacterial species and opens the door for developing novel therapeutics that target PhoQ modulation.

molecular biology↗

bioRxiv2024

Systematic Evaluation of Cell Type Deconvolution Methods for Plasma Cell-free DNA

Plasma cell-free DNA (cfDNA) is derived from cellular death in various tissues. Investigating the origin of cfDNA through tissue/cell type deconvolution allows us to detect changes in tissue homeostasis that occur during disease progression or in response to treatment. Consequently, cfDNA has emerged as a valuable noninvasive biomarker for disease detection and treatment monitoring. Although there are numerous methylation-based methods of cfDNA cell type deconvolution available, a comprehensive and systematic evaluation of these methods has yet to be conducted. In this study, we thoroughly benchmarked five previously published methods: MethAtlas, cfNOMe, CelFiE, CelFEER, and UXM. Utilizing deep whole-genome bisulfite sequencing data from 35 human cell types, we generated cfDNA mixtures with known ground truth to assess the deconvolution performance under various scenarios. Our findings indicate that different factors, including sequencing depth, reference marker selection, and reference completeness, influence cell type deconvolution performance. Notably, omitting cell types present in a mixture from the reference leads to suboptimal results. Despite each method exhibited distinct performances under various scenarios, CelFEER and UXM exhibit overall superior performance compared to the others. In summary, we comprehensively evaluated factors influencing methylation-based cfDNA cell type deconvolution and proposed general guidelines to maximize the performance.

bioinformatics↗

bioRxiv2024

Spatial integration of sensory input and motor output in Pseudomonas aeruginosa chemotaxis through colocalized distribution

The opportunistic pathogen Pseudomonas aeruginosa serves as a model organism for studying multiple signal transduction pathways. The chemoreceptor cluster, a core component of the chemotaxis pathway, is assembled from hundreds of proteins. The unipolar distribution of receptor clusters has long been recognized, yet the precise mechanism governing their assembly remains elusive. Here, we directly observed the relative positions of the flagellar motor and chemoreceptor cluster using flagellar filament labeling and gene editing techniques. Surprisingly, we found that both are located at the same cell pole, with the distribution pattern controlled by the polar anchor protein FlhF. Additionally, the efficient assembly of the chemoreceptor cluster is partially dependent on the integrity of the motor structure. Furthermore, we discovered that overexpression of the chemotaxis regulatory protein CheY leads to high intracellular levels of the second messenger c-di-GMP, triggering cell aggregation. Therefore, the colocalization of the chemoreceptor cluster and flagellum in P. aeruginosa serves to avoid cross-pathway signaling interference, enabling cells to conduct various physiological activities in an orderly manner.

microbiology↗

bioRxiv2024

Heterogeneous hybrid immunity against Omicron variant JN.1 at 11 months following breakthrough infection

A highly transmissible SARS-CoV-2 variant JN.1 is rapidly spreading throughout the nation, becoming the predominant strain in China and worldwide. However, the current immunity against the circulating JN.1 at population level has yet to be fully evaluated. We recruited representative cohorts with stratified age groups and diverse combinations of vaccination and/or infection in recent months, and promptly assessed humoral immunity for these subjects predominantly exhibiting hybrid immunity. We report that at 11 months following BA.5-wave breakthrough infection (BTI), these vaccinated individuals generally showed above-the-threshold yet low level of neutralizing activity against JN.1, with slightly greater potency observed in children and adolescents compared to adults and seniors. Meanwhile, XBB/EG.5-wave reinfection post-BTI significantly boosted the neutralizing antibodies against Omicron variants, including JN.1 in both adults (13.4-fold increase) and seniors (24.9-fold increase). To better understand respiratory mucosal protection against JN.1 over an extended period of months post-BTI, we profiled the humoral immunity in bronchoalveolar lavage samples obtained from vaccinated subjects with or without BTI, and revealed increased potency of neutralizing activity against the BA.5 and JN.1 variants in the respiratory mucosa through natural infection. Notably, at 11 months post-BTI, memory B cell responses against prototype and JN.1 were detectable in both blood and respiratory mucosa, displaying distinct memory features in the circulation and airway compartments. XBB/EG.5-wave reinfection drove the expansion of JN.1-specific B cells, along with the back-boosting of B cells responding to the ancestral viral strain, suggesting the involvement of immune imprinting. Together, this study indicates heterogeneous hybrid immunity over 11 months post-BTI, and underscores the vulnerability of individuals, particularly high-risk seniors, to JN.1 breakthrough infection. An additional booster with XBB-containing vaccine may greatly alleviate the onward transmission of immune-evasive SARS-CoV-2 variants.

immunology↗

bioRxiv2024

Nephrectomy and high-salt diet inducing pulmonary hypertension and kidney damage by increasing Ang II concentration in rats

BackgroundPulmonary hypertension (PH) is a common complication in patients with chronic kidney disease (CKD), affecting prognosis. However, the pathogenesis is not clear, and the lack of a stable animal model is a significant factor. MethodsIn this study, a rat model of chronic kidney disease with pulmonary hypertension (CKD-PH) was developed through 5/6 nephrectomy combined with a high-salt diet. The models hemodynamics and pathological changes in multiple organs were dynamically assessed. Lung tissues and serum were collected from the model rats to measure the expression of ACE2, the expression levels of vascular active components related to the renin-angiotensin-aldosterone system (RAAS), and changes in the serum metabolic profile of the model. ResultsAfter 14 weeks post-surgery, the CKD-PH rat model exhibited significant changes in hemodynamic parameters indicative of pulmonary arterial hypertension, along with alterations such as right ventricular hypertrophy. However, no evidence of pulmonary vascular remodeling was observed. An imbalance in the renin-angiotensin-aldosterone system was identified in the CKD-PH rat models. Downregulation of ACE2 expression was observed in pulmonary tissues. The serum metabolic profile of the CKD-PH rat models showed distinct differences compared to the sham surgery group. ConclusionsThe development of pulmonary arterial hypertension in CKD-PH rats may be primarily attributed to the disruption of the renin-angiotensin-aldosterone system (RAAS), coupled with a decrease in ACE2 expression in pulmonary vascular endothelial tissues and metabolic disturbances.

pathology↗

bioRxiv2024

Cell Type Specific Responses of the Endoplasmic Reticulum Dynamics to Environmental Stress

To overcome the challenge of balancing imaging speecd and resolution, which currently limits the accurate identification of structural and dynamic changes in the study of endoplasmic reticulum (ER) in plant cells. This research employs structured illumination microscopy techniques to achieve super-resolution real-time imaging of the ER in live Arabidopsis materials. Additionally, a self-supervised denoising framework (Blind2Unblind) was optimized to further enhance the signal-to-noise ratio of rapid microscopic imaging. Based on the images with high quality, a method for quantitative analysis of ER structures using time-lapse images is developed. Moreover, detections of changes in ER structures under environmental stress are conducted to verify the effectiveness of the method. Moreover, correlation analyses of various parameters indicate a significant positive correlation between the area and length of tubular ER with the number of growth tips and tricellular junctions, while the area of ER cisternae and bulk flow exhibits a significant negative correlation with the area and length of tubules. The super-resolution imaging and dynamic analysis method developed in this study will provide new technical approaches for further elucidating the function and regulatory mechanisms of the plant ER.

plant biology↗

bioRxiv2023

A cell-free system for target discovery of small membrane proteins

Numerous small proteins have been discovered across all domains of life, among which many are hydrophobic and predicted to localize to the cell membrane. Based on a few that are well-studied, small membrane proteins are regulators involved in various biological processes, such as cell signaling, nutrient transport, drug resistance, and stress response. However, the function of most identified small membrane proteins remains elusive. Their small size and hydrophobicity make protein production challenging, hindering function discovery. Here, we combined a cell-free system with lipid sponge droplets and synthesized small membrane proteins in vitro. Lipid sponge droplets contain a dense network of lipid bilayers, which accommodates and extracts newly synthesized small membrane proteins from the aqueous surroundings. Using small bacterial membrane proteins MgrB, SafA, and AcrZ as proof of principle, we showed that the in vitro produced membrane proteins were functionally active, for example, modulating the activity of their target kinase as expected. The cell-free system produced small membrane proteins, including one from human, up to micromolar concentrations, indicating its high level of versatility and productivity. Furthermore, AcrZ produced in this system was used successfully for in vitro co-immunoprecipitations to identify interaction partners. This work presents a robust alternative approach for producing small membrane proteins, which opens a door to their function discovery in different domains of life. ImportanceSmall membrane proteins are shown to be involved in various biological processes in all domains of life and "can no longer be ignored". Due to their small size and hydrophobicity, functional investigation of small membrane proteins is challenging. In this work, we present a simple, versatile, cell-free approach for synthesizing small membrane proteins in vitro. We show that the small membrane proteins produced with our system are functional and in sufficient amounts for downstream target discoveries. Furthermore, our approach may uncover additional regulatory functions of small membrane proteins studied with conventional methods. Our work provides a robust alternative workflow for functional studies, which opens up new possibilities to advance our understanding of small membrane protein biology.

synthetic biology↗

bioRxiv2023

Melatonin serves as a novel treatment in cystic fibrosis and inhibits cystic fibrosis through TGF-β1/Smad and EMT

BackgroundMelatonin (MEL) is an indole amine molecule primarily produced in the pineal gland. Melatonin has been shown in numerous studies to have anti-fibrosis characteristics in the kidney, liver, and other organs. However, it is still unclear how melatonin works in bladder fibrosis. We explored how melatonin affected animals with bladder fibrosis and its underlying mechanisms. Materials and MethodsMEL was used to treat human bladder smooth muscle cells (HBdSMCs) after they were stimulated with TGF-{beta}1 in vitro. Proteomic analysis and then bioinformatic analysis based on the alterations in these proteins were then performed on HBdSMCs from the different processing methods. To construct an in vivo bladder fibrosis model, we injected protamine sulfate (PS) and lipopolysaccharide (LPS) twice a week into the rat bladder for six weeks. After two weeks of PS/LPS treatment, the treatment group was treated with MEL (20mg/kg/d) for 4 weeks. Finally, we detected the expression of fibrosis markers from different perspectives. The TGF-{beta}1/Smad pathway, and EMT in cell and bladder tissues were also identified. Further proteomic analysis was also performed. ResultsIn the in vitro experiment, we found that TGF-{beta}1 treatment enhanced the fibrosis markers Collagen III and -SMA of HBdSMCs. E-cadherin expression decreased while TGF-{beta}1/Smad pathway was activated. Vimentin and N-cadherin expressions were also elevated at the same time. Similar findings were observed in the LPS group. After MEL treatment, the expression of collagen III and -SMA decreased, and the expression of E-cadherin increased, while the expression of Vimentin and N-cadherin also decreased. CCN1 and SQLE may be the important proteins in the development of bladder fibrosis, according to quantitative proteomics analysis. MEL can decrease their expressions which leadis to relief of bladder fibrosis. Bioinformatics analysis shows that the extracellular space structure related to metabolic pathways, actin filament binding, and stress fibers can serve as a pivotal focus in the management of fibrosis. ConclusionMelatonin attenuates bladder fibrosis by blocking the TGF-{beta}1/Smad pathway and EMT. CCN1 appears to be a possible therapeutic target for bladder fibrosis.

pharmacology and toxicology↗

bioRxiv2023

coRIC map: a framework for the exploration of multifaceted subcellular RNA-binding proteins

The ability of RNA-binding proteins (RBPs) to form complexes with other biomolecules underpins a broad range of functions and remarkable structural properties. Understanding the precise spatiotemporal dynamics of RBPs and their interacting partners in the steady state and upon perturbation is key to deciphering these aspects. Here, we present the coRIC (compartmentalized RNA Interactome Capture) map, an experimental resource and analytical pipeline to study the subcellular dynamics of RBPs through multimodal dataset integration and machine learning. Using this approach, we have generated an atlas comprising 1,768 RBPs distributed in a broad panel of subcellular compartments and delineated their intermolecular and intercompartmental relationships. We have also defined the hierarchy of RBP-containing complexes at multiple scales across the cell, uncovering previously unknown functions of multiple RBPs. Furthermore, we have investigated the changes in RBP complex composition and subcellular distribution in response to C9ORF72 amyotrophic lateral sclerosis/frontotemporal dementia dipeptide repeats and DNA damage stress. The coRIC map provides a valuable new approach for defining the roles of RBPs in homeostasis and disease.

cell biology↗

bioRxiv2023

CryoSTAR: Leveraging Structural Prior and Constraints for Cryo-EM Heterogeneous Reconstruction

Resolving conformational heterogeneity in cryo-electron microscopy (cryo-EM) datasets remains a significant challenge in structural biology. Previous methods have often been restricted to working exclusively on volumetric densities, neglecting the potential of incorporating any pre-existing structural knowledge as prior or constraints. In this paper, we present a novel methodology, cryoSTAR, that harnesses atomic model information as structural regularization to elucidate such heterogeneity. Our method uniquely outputs both coarse-grained models and density maps, showcasing the molecular conformational changes at different levels. Validated against four diverse experimental datasets, spanning large complexes, a membrane protein, and a small single-chain protein, our results consistently demonstrate an efficient and effective solution to conformational heterogeneity with minimal human bias. By integrating atomic model insights with cryo-EM data, cryoSTAR represents a meaningful step forward, paving the way for a deeper understanding of dynamic biological processes.1

biophysics↗